Differential expression of sarcoplasmic proteins in four heterogeneous ovine skeletal muscles

Mass spectrometry-based proteomics approaches to interrogate skeletal muscle adaptations to exercise

Acute exercise and chronic exercise training elicit beneficial whole-body changes in physiology that ultimately depend on profound alterations to the dynamics of tissue-specific proteins. Since the work accomplished during exercise owes predominantly to skeletal muscle, it has received the majority of interest from exercise scientists that attempt to unravel adaptive mechanisms accounting for salutary metabolic effects and performance improvements that arise from training. Contemporary scientists are also beginning to use mass spectrometry-based proteomics, which is emerging as a powerful approach to interrogate the muscle protein signature in a more comprehensive manner. Collectively, these technologies facilitate the analysis of skeletal muscle protein dynamics from several viewpoints, including changes to intracellular proteins (expression proteomics), secreted proteins (secretomics), post-translational modifications as well as fiber-, cell-, and organelle-specific changes. This review aims to highlight recent literature that has leveraged new workflows and advances in mass spectrometry-based proteomics to further our understanding of training-related changes in skeletal muscle. We call attention to untapped areas in skeletal muscle proteomics research relating to exercise training and metabolism, as well as basic points of contention when applying mass spectrometry-based analyses, particularly in the study of human biology. We further encourage researchers to couple the hypothesis-generating and descriptive nature of omics data with functional analyses that propel our understanding of the complex adaptive responses in skeletal muscle that occur with acute and chronic exercise.

Transcriptome analysis revealed potential genes involved in thermogenesis in muscle tissue in cold-exposed lambs

Cold tolerance is an important trait for sheep raised at high altitudes. Muscle tissue, comprising 30–40% of the total body mass, produces heat during cold exposure. However, little is known about the genetic mechanisms of this tissue and its role in thermogenesis in lambs. We examined genes in skeletal muscle tissue in a cold-adapted sheep breed, Altay, and a cold-intolerant sheep breed, Hu, when exposed to low air temperature. Three ewe-lambs of each breed were maintained at −5°C and three ewe-lambs of each breed were maintained at 20°C. After cold exposure for 25 days, the longissimus dorsi of each lamb was collected, and transcriptome profiles were sequenced and analyzed. The results of RNA-seq showed that the average reads among the four groups were 11.0 Gbase. The genome mapping rate averaged 88.1% and the gene mapping rate averaged 82.5%. The analysis of differentially expressed genes (DEGs) indicated that the peroxisome proliferator-activated receptors (PPAR), cAMP, and calcium signaling pathways and muscle contraction in muscle tissue were linked to thermogenesis in cold-exposed lambs. Furthermore, PCK1 (phosphoenolpyruvate carboxykinase1) increased glyceroneogenesis in cold-exposed Altay lambs, and APOC3 (apolipoprotein C3), LPL (lipoprotein lipase), and FABP4 (fatty acid binding protein 4, adipocyte) were involved in the intake and transport of free fatty acids. In Hu sheep, cAMP biosynthesis from ATP hydrolysis was regulated by ADCY10 (adenylate cyclase) and ADORA2a (adenosine A2a receptor). Skeletal muscle contraction was regulated by MYL2 (myosin light chain 2). In conclusion, cold exposure altered the expression level of genes involved in heat production in muscle tissue. Some potential mechanisms were revealed, including calcium ion transport in the calcium signaling pathway, fatty acid metabolism in the PPAR signaling pathway, and cAMP biosynthesis in the cAMP signaling pathway. This study implied that skeletal muscle plays an important role in thermoregulation in lambs.

Non-thermal processing has an impact on the digestibility of the muscle proteins

Muscle proteins undergo several processes before being ready in a final consumable form. All these processes affect the digestibility of muscle proteins and subsequent release of amino acids and peptides during digestion in the human gut. The present review examines the effects of different processing techniques, such as curing, drying, ripening, comminution, aging, and marination on the digestibility of muscle proteins. The review also examines how the source of muscle proteins alters the gastrointestinal protein digestion. Processing techniques affect the structural and functional properties of muscle proteins and can affect their digestibility negatively or positively depending on the processing conditions. Some of these techniques, such as aging and mincing, can induce favorable changes in muscle proteins, such as partial unfolding or exposure of cleavage sites, and increase susceptibility to hydrolysis by digestive enzymes whereas others, such as drying and marination, can induce unfavorable changes, such as severe cross-linking, protein aggregation, oxidation induced changes or increased disulfide (S-S) bond content, thereby decreasing proteolysis. The underlying mechanisms have been discussed in detail and the conclusions drawn in the light of existing knowledge provide information with potential industrial importance.

Metabolites and Metabolic Pathways Correlated With Beef Tenderness

Metabolite profile has been used to understand the causes of variability in beef tenderness, but still little is known about how metabolites contribute to beef quality. Therefore, this study was carried out to evaluate how meat metabolites and their metabolic pathways correlate to variability in beef tenderness. Carcasses from 60 noncastrated male cattle were selected, and three 2.5-cm-thick longissimus thoracis steaks were obtained and aged (0°C to 4°C) for 7d. Warner-Bratzler shear force (WBSF) was performed (steak 1). Based on WBSF data, 2 tenderness classes (n = 30; 15 per class [tender and tough]) were created to perform sarcomere length (steak 2) and metabolom ic analysis (steak 3). Meat ultimate pH did not differ between tenderness classes. However, steaks classified as tender had greater sarcomere length (P = 0.019) than those classified as tough. Acetyl-carnitine (P = 0.026), adenine (P = 0.026), beta-alanine (P = 0.005), fumarate (P = 0.022), glutamine (P = 0.043), and valine (P = 0.030) concentration were higher in tender beef compared with tough beef. The 4 most important compounds differing between tender and tough beef were lactate, glucose, creatine, and glutamine, which may indicate that metabolic pathways such as D-glutamine and D-glutamate metabolism, beta-alanine metabolism, purine metabolism, and tricarboxylic acid cycle affected the tenderness classes. Beta-alanine (r = − 0.45), acetyl-carnitine (r = − 0.40), fumarate (r = − 0.38), valine (r = − 0.34), glucose (r = − 0.32), glutamine (r = − 0.31), and adenine (r = −0.31) were negatively correlated with WBSF values. Metabolite profile in tender beef indicated a greater oxidative metabolism, which promoted modifications in the muscle structure and proteolysis, favoring its tenderization.

Proteomic analysis to investigate color changes of chilled beef longissimus steaks held under carbon monoxide and high oxygen packaging

This study investigated the proteome basis for color stability variations in beef steaks packaged under two modified atmosphere packaging (MAP) methods: HiOx-MAP (80% O₂/20% CO₂) and CO-MAP (0.4% CO/30% CO₂/69.6% N₂) during 15 days of storage. The color stability, pH, and sarcoplasmic proteome analysis of steaks were evaluated on days 0, 5, 10 and 15 of storage. Proteomic results revealed that the differential expression of the sarcoplasmic proteome during storage contributed to the variations in meat color stability between the two MAP methods. Compared with HiOx-MAP steaks, some glycolytic and energy metabolic enzymes important in NADH regeneration and antioxidant processes, antioxidant peroxiredoxins (thioredoxin-dependent peroxide reductase, peroxiredoxin-2, peroxiredoxin-6) and protein DJ-1 were more abundant in CO-MAP steaks. The over-expression of these proteins could induce CO-MAP steaks to maintain high levels of metmyoglobin reducing activity and oxygen consumption rate, resulting in CO-MAP steaks exhibiting better color stability than HiOx-MAP steaks during storage.

Comparative Proteomic and Transcriptomic Analysis of Follistatin-Induced Skeletal Muscle Hypertrophy

Skeletal muscle, the most abundant body tissue, plays vital roles in locomotion and metabolism. Myostatin is a negative regulator of skeletal muscle mass. In addition to increasing muscle mass, Myostatin inhibition impacts muscle contractility and energy metabolism. To decipher the mechanisms of action of the Myostatin inhibitors, we used proteomic and transcriptomic approaches to investigate the changes induced in skeletal muscles of transgenic mice overexpressing Follistatin, a physiological Myostatin inhibitor. Our proteomic workflow included a fractionation step to identify weakly expressed proteins and a comparison of fast versus slow muscles. Functional annotation of altered proteins supports the phenotypic changes induced by Myostatin inhibition, including modifications in energy metabolism, fiber type, insulin and calcium signaling, as well as membrane repair and regeneration. Less than 10% of the differentially expressed proteins were found to be also regulated at the mRNA level but the Biological Process annotation, and the KEGG pathways analysis of transcriptomic results shows a great concordance with the proteomic data. Thus this study describes the most extensive omics analysis of muscle overexpressing Follistatin, providing molecular-level insights to explain the observed muscle phenotypic changes.

Proteomic approach to characterize biochemistry of meat quality defects

Proteomics can be used to characterize quality defects including pale, soft, and exudative (PSE) meat (pork and poultry), woody broiler breast meat, reddish catfish fillets, meat toughness, and beef myoglobin oxidation. PSE broiler meat was characterized by 15 proteins that differed in abundance in comparison to normal broiler breast meat, and eight proteins were differentially expressed in woody breast meat in comparison to normal breast meat. Hemoglobin was the only protein that was differentially expressed between red and normal catfish fillets. However, inducing low oxygen and/or heat stress conditions to catfish fillets did not lead to the production of red fillets. Proteomic data provided information pertaining to the protein differences that exist in meat quality defects. However, these data need to be evaluated in conjunction with information pertaining to genetics, nutrition, environment of the live animal, muscle to meat conversion, meat quality analyses and sensory attributes to understand causality, protein biomarkers, and ultimately how to prevent quality defects.

The sheep (Ovis aries) muscle proteome: Decoding the mechanisms of tolerance to Seasonal Weight Loss using label-free proteomics

Seasonal Weight Loss (SWL) is one of the most pressing issues in animal production in the tropics and Mediterranean. This work aims to characterize muscle proteome changes as a consequence of SWL in meat producing sheep, using a label-free proteomics approach. We compare three breeds: the Australian Merino (SWL susceptible), the Damara (SWL tolerant) and the Dorper (SWL intermediate tolerance). We identified 668 proteins of the sheep proteome, 95 with differential regulation. Also we observe that the more vulnerable to SWL a breed is, the more differential abundance proteins we find. Protein binding was the most frequently altered molecular function identified. We suggest 6 putative markers for restricted nutritional conditions independently of breed: ferritin heavy-chain; immunoglobulin V lambda chain; transgelin; fatty acid synthase; glutathione S-transferase A2; dihydrodiol dehydrogenase 3-like. Moreover, we suggest as related to SWL tolerance: S100-A10 Serpin A3-5-like and Catalase, subject however to necessary validation assays. The identification of SWL-tolerance related proteins using proteomics will lead to increased stock productivity of relevant interest to animal production, particularly if identified at the muscle level, the tissue of economic importance in meat production.

BIOLOGICAL SIGNIFICANCE

Seasonal Weight Loss (SWL) is the most pressing issue in animal production in the tropics and the Mediterranean. To counter SWL, farmers often use animal breeds that have a natural ability to withstand pasture scarcity. Here we study the sheep muscle proteome at the muscle level, the tissue of economic importance in meat production. Furthermore, the identification of proteins that change their abundance in response to SWL using proteomics can contribute to increased stock productivity of relevant interest to animal production. We identified 668 proteins of the sheep proteome. We demonstrate that the following proteins are affected by restricted nutritional conditions: ferritin heavy chain; immunoglobulin V lambda chain; transgelin; fatty acid synthase; glutathione S-transferase A2; dihydrodiol dehydrogenase 3-like. Furthermore, S100-A10, Serpin A3-5-like and Catalase are proteins that changed their abundance in response to SWL. Nevertheless, it is important to highlight that Catalase values for the merino breed were close to significance and therefore catalase validation is of utmost importance.

Lipid profiles of adipose and muscle tissues in mouse models of juvenile onset of obesity without high fat diet induction: a Fourier transform infrared (FT-IR) spectroscopic study

The current study aims to determine lipid profiles in terms of the content and structure of skeletal muscle and adipose tissues to better understand the characteristics of juvenile-onset spontaneous obesity without high fat diet induction. For the purposes of this study, muscle (longissimus, quadriceps) and adipose (inguinal, gonadal) tissues of 10-week-old male DBA/2J and Berlin fat mouse inbred (BFMI) lines (BFMI856, BFMI860, BFMI861) fed with a standard breeding diet were used. Biomolecular structure and composition was determined using attenuated total reflection Fourier transform (ATR FT-IR) spectroscopy, and muscle triglyceride content was further quantified using high-performance liquid chromatography (HPLC) coupled with an evaporative light scattering detector (ELSD). The results revealed a loss of unsaturation in BFMI860 and BFMI861 lines in both muscles and inguinal adipose tissue, together with a decrease in the hydrocarbon chain length of lipids, especially in the BFMI860 line in muscles, suggesting an increased lipid peroxidation. There was an increase in saturated lipid and triglyceride content in all tissues of BFMI lines, more profoundly in longissimus muscle, where the increased triglyceride content was quantitatively confirmed by HPLC-ELSD. Moreover, an increase in the metabolic turnover of carbohydrates in muscles of the BFMI860 line was observed. The results demonstrated that subcutaneous (inguinal) fat also displayed considerable obesity-induced alterations. Taken together, the results revealed differences in lipid structure and content of BFMI lines, which may originate from different insulin sensitivity levels of the lines, making them promising animal models for spontaneous obesity. The results will contribute to the understanding of the generation of insulin resistance in obesity without high fat diet induction.

Differential Proteome Analysis of Breast and Thigh Muscles between Korean Native Chickens and Commercial Broilers

The Korean native chickens (Woorimotdak™, KNC) and commercial broilers (Ross, CB) show obvious differences in meat flavor after cooking. To understand the contribution of protein and peptide for meat flavor, 2-dimensional (2-D) gel electrophoresis and matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry was performed. A total of 16 protein spots were differentially expressed in the breast and thigh meat between the two breeds. A total of seven protein spots were represented by different levels between KNC and CB for breast meat. Among them three protein spots (TU39149, TU40162 and TU39598) showed increases in their expressions in KNC while other four protein spots (BU40125, BU40119, BU40029 and BU39904) showed increases in CB. All nine protein spots that were represented by different levels between KNC and CB for thigh meat showed increases in their expression in KNC. Phosphoglucomutase 1 (PGM 1), myosin heavy chain (MyHC), heat shock protein B1 (HSP27), cytochrome c reductase (Enzyme Q), Glyoxylase 1, DNA methyltransferase 3B (DNA MTase 3) were identified as the main protein spots by MALDI-TOF mass spectrometry. These results can provide valuable basic information for understanding the molecular mechanism responsible for breed specific differences in meat quality, especially the meat flavour.

Proteomics of muscle-specific beef color stability

The objective of the present study was to differentiate the sarcoplasmic proteome of color-stable (Longissimus lumborum; LL) and color-labile (Psoas major; PM) beef muscles. LL and PM muscles from seven beef carcasses (24 h post-mortem) were fabricated into 2.54 cm steaks, aerobically packaged, and assigned to refrigerated retail display for 9 days. LL steaks demonstrated greater (P < 0.05) color stability and lower (P < 0.05) lipid oxidation than PM steaks. Proteome analyses identified 16 differentially abundant proteins in LL and PM, including antioxidant proteins and chaperones. Proteins demonstrating positive correlation with redness (aldose reductase, creatine kinase, and β-enolase) and color stability (peroxiredoxin-2, peptide methionine sulfoxide reductase, and heat shock protein-27 kDa) were overabundant in LL, whereas the protein overabundant in PM (mitochondrial aconitase) exhibited negative correlation with redness. The color stability of LL could be attributed to the overabundance of antioxidant proteins and chaperones, and this finding suggests the necessity of developing muscle-specific processing strategies to improve beef color.

Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques

Background

Skeletal muscle fibres represent one of the most abundant cell types in mammals. Their highly specialised contractile and metabolic functions depend on a large number of membrane-associated proteins with very high molecular masses, proteins with extensive posttranslational modifications and components that exist in highly complex supramolecular structures. This makes it extremely difficult to perform conventional biochemical studies of potential changes in protein clusters during physiological adaptations or pathological processes.

Results

Skeletal muscle proteomics attempts to establish the global identification and biochemical characterisation of all members of the muscle-associated protein complement. A considerable number of proteomic studies have employed large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography, and combined them with mass spectrometry as the method of choice for high-throughput protein identification. Muscle proteomics has been applied to the comprehensive biochemical profiling of developing, maturing and aging muscle, as well as the analysis of contractile tissues undergoing physiological adaptations seen in disuse atrophy, physical exercise and chronic muscle transformation. Biomedical investigations into proteome-wide alterations in skeletal muscle tissues were also used to establish novel biomarker signatures of neuromuscular disorders. Importantly, mass spectrometric studies have confirmed the enormous complexity of posttranslational modifications in skeletal muscle proteins.

Conclusions

This review critically examines the scientific impact of modern muscle proteomics and discusses its successful application for a better understanding of muscle biology, but also outlines its technical limitations and emerging techniques to establish new biomarker candidates.

Isolation, purification and characterization of antioxidant peptidic fractions from a bovine liver sarcoplasmic protein thermolysin hydrolyzate

Sarcoplasmic proteins isolated from bovine livers were hydrolyzed using the enzyme thermolysin at 37°C for 2h. The hydrolyzates were filtered through molecular weight cut off membranes (MWCO) and filtrates were obtained. The water activity (a(w)) of unhydrolysed sarcoplasmic protein, full hydrolyzates, 10-kDa and 3-kDa filtrates were below the limit necessary for microbial growth. The antioxidant activities of both filtrates and fractions were assessed using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity assay, the ferric ion reducing antioxidant power (FRAP) assay and the Fe(2+) chelating ability assay. RP-HPLC was used for purification of the full hydrolyzates, the 10-kDa and the 3-kDa filtrates. The peptidic content of the full hydrolyzates, the 10-kDa and the 3-kDa filtrates were assessed using the Dumas method and peptide contents of each fraction were characterized using electrospray quadrupole time-of-flight (ESI-Q-TOF) mass spectrometry with the resultant spectrum analysed using the software programmes Protein Lynx Global Server 2.4. and TurboSEQUEST. Similarities between the amino acid composition of characterized peptides from each fraction and previously reported antioxidant peptides were found. This study demonstrates that meat by-product such as liver can be utilised as raw material for the generation of bioactive peptides with demonstrated antioxidant activities in vitro using the enzyme thermolysin. It is significant as it presents a potential opportunity for meat processors to use their waste streams for the generation of bioactive peptides for potential functional food use.

Proteomics of skeletal muscle differentiation, neuromuscular disorders and fiber aging

Skeletal muscle fibers are the most abundant cellular structure in the human body. Altered neuromuscular activity, traumatic injury or genetic abnormalities have profound effects on muscle integrity, tissue mass, fiber type distribution, metabolic integration and contractile function. The recent application of mass spectrometry-based proteomics has decisively advanced our molecular understanding of numerous physiological adaptations in healthy muscle and pathophysiological mechanisms associated with major muscle diseases. Skeletal muscle proteomics promises to play a major role in the establishment of a disease-specific biomarker signature for the major classes of neuromuscular disorders. New muscle markers will be crucial for the development of improved diagnostics, the monitoring of disease progression, evaluation of drug action and the identification of novel therapeutic targets.

Oxidative stress regulation of stem and progenitor cells

In recent years, it has become clear that balanced regulation of reactive oxygen species is of critical significance for cell-fate determination as well as for stem cell development, function, and survival. Although many questions regarding intracellular redox status regulation of stem cell fate remain, we review here what is known regarding the impact of cell-fate signaling as shown with a variety of human cancer cells and more recently on cancer-initiating cells and on the regenerative capacity of skeletal muscle and hematopoietic tissue and their stem cells. We also discuss the role of altered intracellular redox status as a potential primary pathogenic mechanism in muscular dystrophy and hematopoietic pathologies. Studies discussed here illustrate how understanding altered redox regulation of stem cell behavior may contribute to the development of novel stem cell therapies.

Differential expression of sarcoplasmic and myofibrillar proteins of rat soleus muscle during denervation atrophy

Denervation is known to induce skeletal muscle atrophy and fiber-type transitions, the molecular mechanisms of which are poorly understood. To investigate the effect of denervation on skeletal muscle, proteomic analysis was performed to compare denervated soleus muscle with normal soleus muscle. The muscles were fractionated to myofibrillar and sarcoplasmic fractions, which were analysed using two-dimensional gel electrophoresis (2-DE), followed by MALDI-TOF-MS. At least 30 differentially regulated proteins were identified in the sarcoplasmic fractions of normal and denervated soleus muscles. This group included metabolic enzymes, signaling molecules, chaperones, and contractile proteins. We also found two proteins, APOBEC-2 (RNA-editing enzyme) and Gamma-synuclein (breast cancer related protein), which have not been recognized as denervation-induced proteins to date. Our results might prove to be beneficial in elucidating the molecular mechanisms of denervation-induced muscle atrophy.

MicroRNA transcriptome profiles during swine skeletal muscle development

Background

MicroRNA (miR) are a class of small RNAs that regulate gene expression by inhibiting translation of protein encoding transcripts. To evaluate the role of miR in skeletal muscle of swine, global microRNA abundance was measured at specific developmental stages including proliferating satellite cells, three stages of fetal growth, day-old neonate, and the adult.

Results

Twelve potential novel miR were detected that did not match previously reported sequences. In addition, a number of miR previously reported to be expressed in mammalian muscle were detected, having a variety of abundance patterns through muscle development. Muscle-specific miR-206 was nearly absent in proliferating satellite cells in culture, but was the highest abundant miR at other time points evaluated. In addition, miR-1 was moderately abundant throughout developmental stages with highest abundance in the adult. In contrast, miR-133 was moderately abundant in adult muscle and either not detectable or lowly abundant throughout fetal and neonate development. Changes in abundance of ubiquitously expressed miR were also observed. MiR-432 abundance was highest at the earliest stage of fetal development tested (60 day-old fetus) and decreased throughout development to the adult. Conversely, miR-24 and miR-27 exhibited greatest abundance in proliferating satellite cells and the adult, while abundance of miR-368, miR-376, and miR-423-5p was greatest in the neonate.

Conclusion

These data present a complete set of transcriptome profiles to evaluate miR abundance at specific stages of skeletal muscle growth in swine. Identification of these miR provides an initial group of miR that may play a vital role in muscle development and growth.

Muscle-derived ROS and thiol regulation in muscle fatigue

Muscles produce oxidants, including reactive oxygen species (ROS) and reactive nitrogen species (RNS), from a variety of intracellular sources. Oxidants are detectable in muscle at low levels during rest and at higher levels during contractions. RNS depress force production but do not appear to cause fatigue of healthy muscle. In contrast, muscle-derived ROS contribute to fatigue because loss of function can be delayed by ROS-specific antioxidants. Thiol regulation appears to be important in this biology. Fatigue causes oxidation of glutathione, a thiol antioxidant in muscle fibers, and is reversed by thiol-specific reducing agents. N-acetylcysteine (NAC), a drug that supports glutathione synthesis, has been shown to lessen oxidation of cellular constituents and delay muscle fatigue. In humans, NAC pretreatment improves performance of limb and respiratory muscles during fatigue protocols and extends time to task failure during volitional exercise. These findings highlight the importance of ROS and thiol chemistry in fatigue, show the feasibility of thiol-based countermeasures, and identify new directions for mechanistic and translational research.